In the books

In the A Song of Ice and Fire novels, Rhaegar is depicted as a chivalrous, honorable, well loved by the smallfolk and just warrior, albeit one often distracted by other concerns and apparently unable or unwilling to restrain the worst excesses of his father. The only person who genuinely hated Rhaegar was Robert Baratheon. Rhaegar had silver-gold hair and dark lilac eyes. He was considered to be tall and handsome. Cersei Lannister, who was infatuated with him, remembers Rhaegar as the most beautiful man she had ever seen. Rhaegar was very bookish in his youth, such that people jested that the Queen swallowed some books and a candle while he was in her wombs. As a boy he was able to impress the maesters with his wit. He was married to Princess Elia Martell of Dorne, with whom he had two children, Rhaenys and Aegon. It is suggested that he was not in love with Elia but was content in his marriage nonetheless.

Rhaegar's reasons for kidnapping Lyanna Stark remain a mystery to both his supporters and his detractors, but the entire realm knows that they had met at a great tourney at the castle of Harrenhal a year before the kidnapping. Rhaegar had crowned her Queen of Love and Beauty, passing over his wife.

One of the main reasons that the other noble Houses of the realm put up with King Aerys' increasing madness for as long as they did is because Rhaegar was widely loved and respected by all, and it was believed he would make a great king. Most were willing to simply wait out the rest of Aerys' reign until his son succeeded him, rather than deal with the controversy of rebelling against and killing a king. It was therefore a great shock when Rhaegar absconded with Lyanna Stark, but even so, royalists in the civil war weren't primarily fighting out of loyalty to Mad King Aerys, but out of loyalty to Prince Rhaegar. Thus when Rhaegar died in the Battle of the Trident, the Targaryen cause was doomed, and not simply due to a decisive military defeat. Without Rhaegar, Aerys's allies began to slip away, and it was only after the defeat at the Battle of the Trident that the Lannisters turned on the Targaryens, resulting in the Sack of King's Landing and the death of Aerys.

When Daenerys Targaryen was in the House of the Undying, one of the visions she saw was a man resembling Viserys but taller than him, with dark indigo eyes, and a woman nursing a newborn babe in a great wooden bed. Both Daenerys and the readers believe them to be Rhaegar, Elia, and their infant son Aegon.